CDATA showing up at end of output files

This seems like a newbie question, but I couldn't find the answer on
google.
I've been using xsl to transform rdf files into runnable
programs in another (non-markup) language. It's been great except for a
minor hiccup - all text within CDATA blocks shows up at the end of my
output files without being invited.
I think I've boiled it down to a specific problem, but I'd like to better
understand why it is a problem at all.

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